Well, I don’t like when my PC goes beep-beep at 2 a.m. and everybody is sleeping! So I’ve found a radical way to disable it: simply forbidding Linux to load the PC speaker kernel module.
Edit /etc/rc.local and add:
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rmmod pcspkr
That’s it.
If you want to disable it right now simply type the same line in a terminal, as root (or use sudo):
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# rmmod pcspkr